Tuesday, April 20, 2010

The Stickleback and Confirmation Bias

Species of stickleback fish can rapid adapt to new environments. Such adaptations can range from minor adjustments to body shape and size to the complete loss of major structures such as the pelvis. It is an example of rapid, intelligent adaptation, not the sort of change expected by evolution.

This is not the only surprise for evolutionists. Recent research has found that these adaptations are controlled by different genes. That surprised evolutionists because they expect the same genes would control the same changes in related species. A basic prediction of evolution is that related species should be genetically similar, because they have been evolving independently for only a relatively short period. But this expectation is routinely contradicted by biology, which seems to be unaware of the theory of evolution.

Another interesting example of this in stickleback fish are the sex-determination genes, which are located on different chromosomes in different species. As one evolutionist admitted:

This is very surprising because these species are fairly closely related.

Evolutionists believe that significant differences such as these must have somehow evolved. Evolutionists may not have a clear or compelling explanation for how or why the change came about, but not surprisingly, they believe evolution did the job. Since these differences do not fit the evolutionary expectation, they are viewed as anomalies, whereas the similarities that are expected are viewed as more informative of evolutionary relationship. It is the latter, not the former, that are more often used when evolutionists create their evolutionary trees.

This pre screening of data is known as confirmation bias. It is a well known tendency in science. Proponents of a theory are less likely to dwell on, or perhaps even acknowledge, contradictory data. Those data are viewed as outliers. This is one reason why objective theory evaluation is difficult. Don't expect evolutionists to tell us one day that their theory may not be a fact after all, even though that is what the science tells us.

21 comments:

What seems to be a problem with this site can be summed up by the problem with one of your links:

http://www.darwinspredictions.com

Basically the argument is that evolution is falsified so many times, yet evolutionsts persist in making excuses, fiddling with the theory to make it fit the facts; and that the great number of falsifications should really be nails in the coffin of evolution; and therefore God exists.

But that's not how it works. Many of issues raised on that site and this are not falsifications of evolution.

When scientist is trying to figure something out they come up with a hypothesis. As Richard Feynman said, it can be just a guess, though it's usually a guess based on previous insight, not just some random idea.

The next step is to come up with some experiments to test the hypothesis, sometimes in an attempt to confirm it, but better still are tests that attempt to falsify it.

This is the process of science. And just because some discoveries have more complex mechanisms or strutures than expected is no surprise.

Theists complain that all this shows evolution to be false. But it doesn't. Nothing has yet falsified the basic idea of evolution by natural selection acting on change.

The results of the complete falsification of evolution would lead to a new theory. Maybe some other hypotheses would need to be considered.

How about the hypothesis, God did it. Well, it's an option. Right then. Precisely what tests are you going to construct to support it? How would you go about falsifying the theory that predicts there is life after death. We all know you have nothing.

All you can do point at real scientific progress, real learning, identify some ideas that turned out to be wrong, and imply that this shows God did it. But the irony is that if scientists did get every hypothesis right, and every experiment confirmed the theory it was testing, if science never got anything wrong, then this would be a better indication that God was guiding us.

But each such test falsified the theory. Every hypothesys that stood at the basis of evolunioary theory from radiometric dating, to index fossils, to homology has already been falsified. Then why does this theory does not die already?

Ron:The next step is to come up with some experiments to test the hypothesis, sometimes in an attempt to confirm it, but better still are tests that attempt to falsify it.

The problem is that that the major claim of the theory of evolution cannot be tested, at least not in the way I think you mean.

The major claim is that all of life's history, diversity, and complexity can be explained by random, undirected processes and natural selection. These processes played out over thousands and thousands of years.

Obviously, no one can run an experiment that takes that long. This puts the theory of evolution in the realm of the historical sciences.

What framework would you use to arrive at the conclusion that the theory of evolution is the best explanation for the history of life?

Interesting the data was pre-screened/hidden/denied, yet published in a peer-reviewed journal. Which is it-does science ignore and hide the data, or do all these little snippets (that show there is debate and conversation and curiosity and surprise in science) that Dr. Hunter posts contradict that?

"Obviously, no one can run an experiment that takes that long. This puts the theory of evolution in the realm of the historical sciences."

Evolution has both historical (molecular phylogeny, organelles, fossil record) AND experimental data supporting it. For example, scientists could take sticklebacks from salt water, place them in fresh, and watch them evolve:

http://www.sciencemag.org/cgi/content/full/322/5899/255

"Experimental estimates of the effects of selection on genes determining adaptive traits add to our understanding of the mechanisms of evolution. We measured selection on genotypes of the Ectodysplasin locus, which underlie differences in lateral plates in threespine stickleback fish. A derived allele (low) causing reduced plate number has been fixed repeatedly after marine stickleback colonized freshwater from the sea, where the ancestral allele (complete) predominates. We transplanted marine sticklebacks carrying both alleles to freshwater ponds and tracked genotype frequencies over a generation. The low allele increased in frequency once lateral plates developed, most likely via a growth advantage. Opposing selection at the larval stage and changing dominance for fitness throughout life suggest either that the gene affects additional traits undergoing selection or that linked loci also are affecting fitness"

Yeah, I know, they didn't make a dog from a fish. But with this, and other experimental data, if the mechanisms for evolution can be experimentally confirmed, and the historical evidence is there, what do we conclude?

Variation is not the same with evolution. Shuffling a deck of cards is not the same as inventing a new card. Evolution needs a method to invent new cards (new genes). Shuffling existing genes around and losing some is not a mechanism for it.

For example, scientists could take sticklebacks from salt water, place them in fresh, and watch them evolve:

What? You mean we could see new genetic information being added to the genome?

Wow!

Or are you using another definition of evolution -- and doing what Phil Johnson pointed out -- committing the fallacy of equivocation? Yes, I think you are probably using multiple definitions of evolution and switching between them as you please.

Cornelius says: "Evolutionists believe that significant differences such as these must have somehow evolved. Evolutionists may not have a clear or compelling explanation for how or why the change came about, but not surprisingly, they believe evolution did the job. Since these differences do not fit the evolutionary expectation, they are viewed as anomalies, whereas the similarities that are expected are viewed as more informative of evolutionary relationship. It is the latter, not the former, that are more often used when evolutionists create their evolutionary trees.

This is a classic Hunter Distortion. An interesting case study discussed in the literature suddenly becomes a Serious Problem For Evolution which clearly demonstrates the dishonesty and/or incompetency of evolutionary biologists.

It may be unusual for sex-determining genes to have been rearranged in sticklebacks, but it is incorrect to state that evolutionary theory has no answer for this. And yet of course, if I present an answer, Cornelius will reflexively claim that evolutionary theory is simply a pile of post hoc add-ons. Evolutionary theory is wrong either because it can't explain such phenomena or because it can. Genius.

In posts such as the previous one, http://darwins-god.blogspot.com/2010/04/histone-variants-incredible-story-of.html, Cornelius presents complexity as evidence against evolution, yet any complexity in evolutionary theory itself invalidates it.

There are in fact far more radical examples of genomic rearrangement within genera than this in the literature. Such rearrangements might reinforce reproductive isolation, but they are still only the shuffling of genomes. This does not mean species are no longer "genetically similar" and it is not a devastating blow to evolution.

"Proponents of a theory are less likely to dwell on, or perhaps even acknowledge, contradictory data."

This may well often be true. But scientists who engage is such practices are unlikely to ever be very good at what they do. On the other hand, I regularly read literature where the problem examples for evolution are openly and honestly discussed and wrestled with. The first step is to try and work out what is happening at the proximate level. Then see how this fits/doesn't fit with surrounding theory.

Such examples often tell us much about real evolutionary processes and sometimes lead to major shifts in thinking. As yet, no one has rejected the whole of evolutionary theory based on an anomaly, as such a rejection is not warranted.

Believe it or not, scientists are normally motivated by a desire to understand the natural world, not by a compulsion to lie to the public.

Evolution is "the change in the inherited traits of a population of organisms through successive generations."Futuyma, Douglas J. (2005). Evolution. Sunderland, Massachusetts: Sinauer Associates, Inc. ISBN 0-87893-187-2.

Directly observed in sticklebacks. The inherited trait of plating changes over successive generations under selective pressure.

"What? You mean we could see new genetic information being added to the genome? "

Not sure what 'information' has to do with it. You guys throw that word around pretty loosely over here. Are you defining evolution as a gain in information content? I could give experimental and real-world examples of gain-of-function mutations. Or can only the designer do that?

You tell me:1) Was information added?Or2) Can animals evolve novel traits without gain of information?

Who is Phil Johnson? Never heard of him, nor do I know what argument you might be referencing.

The Tree of Life was suppose to be evidence for evolution. Animals that are similar morhologically have a more recent common ancestor. But if the DNA doesn't match the morphologies, that becomes a problem that evolution has to explain.

I understand that a lot of the chnages observed in sticklebacks come from the loss of function of a gene. If anything, this is only an example of devolution. It doesn't follow from here that an organism can gain some function or structure by the same process.

"the change in the inherited traits of a population of organisms through successive generations."

I can agree to that because there is no requirement of universal common descent. This definition is compatible with intelligent design, evolution, theistic evolution, and creationism which accepts adaptions to the environment.

Evolution has both historical (molecular phylogeny, organelles, fossil record) AND experimental data supporting it. For example, scientists could take sticklebacks from salt water, place them in fresh, and watch them evolve:

The theory of evolution relies on equivocation. I can throw rocks at a car. The act of doing so experimentally demonstrates that the care experiences "change over time" threw this mechanism. It hardly makes a convincing case that this is the mechanisms which caused the car to exist in the first place.

Yet such non-sequiturs arguments are par for the course in defending evolutionary theory.

Observed laboratory evolution hardly constitutes the level of change needed for the grand claims of Evolutionists. One thing we've also observed in the lab are LIMITS to change. Confirmation bias ignores these empirical results as well. Yet these results would cast doubt on evolutionary theories, but they are ignored.

"I can throw rocks at a car. The act of doing so experimentally demonstrates that the care {sic} experiences "change over time" threw {sic} this mechanism. It hardly makes a convincing case that this is the mechanisms {sic} which caused the car to exist in the first place."

False analogy and circular logic. Is this all ID has? Pathetic. To prove design, you compare life to a designed inanimate object. Cars don't reproduce. Cars don't live or develop. Cars aren't composed of cells containing the same genetic information. The history of cars doesn't form a nested hierarchy. Why don't you design a car for me? Make it up of cells that develop from a single bolt(?) using inheritable instructions, and I'll test whether it can evolve for you.

"Observed laboratory evolution hardly constitutes the level of change needed for the grand claims of Evolutionists. One thing we've also observed in the lab are LIMITS to change."

And what are those limits? Enough to make HIV drug resistant in a single person? Enough to make malaria drug resistant (Behe doesn't think so)? Enough to cause gain of function/information mutations in leukemia in tens of thousands of children a year? Is the designer performing all these miracles for us? Or is evolution more potent than you wish?

Novel functions have been developed. Evolution has been observed. Mechanisms have been tested. Have we recapitulated the entire history of life in the last few decades? Of course not. Have we tested the mechanisms, with clearer and clearer understandings of the implications? Yes. Do these lab studies correlate and explain the historical data? Yes.

Does design have a explanation for nested hierarchies in phylogeny?

What about molecular co-evolution? Why aren't co-evolving pairs of proteins or motifs 'designed' around at some point?

Natch-"But if the DNA doesn't match the morphologies, that becomes a problem that evolution has to explain."

Could you give me an example where a morphological phenotype does not ultimately derive from genotype?

"I understand that a lot of the chnages observed in sticklebacks come from the loss of function of a gene."

So, we can have evolution without gain of function? Interesting for the information types who insist there must be information gain. And, again, there are plenty of gain-of-function mutations observed in nature. Did the designer contribute directly to these, but not the stickleback, who has inactivating mutations? Did the stickleback, therefore, find its freshwater life naturally?

By the way, is our loss of hair and strength 'devolution' from apes? Unlike designs, evolution doesn't have a goal-just selection for organisms that fit their niche. There is no such thing as 'devolution;, just the next organism in the chain of being.

But is it possible to infer from cases of loos of function that evolution via a gain in is possible?

Studying selection doesn't depend on gain or loss of function. The molecular mechanisms can be similar. But, we can also look at gain of functions in evolution experiments. Nylon and citrate utilizing bacteria, drug resistant plants, bacteria, viruses and parasites, curly coat genes in dogs, come to mind.

We can infer, and then test, other gain of functions mutations through phylogeny. Hox genes have been swapped between organisms, with profound changes to body plan, for example.

RobertC:Yeah, I know, they didn't make a dog from a fish. But with this, and other experimental data, if the mechanisms for evolution can be experimentally confirmed, and the historical evidence is there, what do we conclude?

As someone once said, that is a most excellent question. To phrase the question more succinctly, is it legitimate to extrapolate from the evidence we can observe to the conclusion that those mechanisms can also explain the major morphological changes seen in the fossil record?

I emphasize "changes" because change implies a gradual transition from one form to another. The fossil record does not seem to confirm this.

From the Cambrian explosion to the fossil record in general, we see the abrupt appearance of new morphological forms with little change until they disappear from the fossil record. Missing are all the failed evolutionary experiments one would think should be there.

To use an engineering analogy, to change an assembly line from manufacturing automobiles to manufacturing boats is orders of magnitude different from changing the style of the wheels or the grille on an exitisting automobile.

I have not read much about developmental biology, but it seems to me that science cannot begin to speculate about what it takes to re-engineer an organism until it knows how an organism is built in the first place.

One thing I did read is that the body plan for an organism does not reside in the genome. If not, where does it reside, and how does it govern the assembly of all the proteins specified by the genome into the final body plan?

And if the genome specifies only proteins then mutations cannot account for new body plans.

"I emphasize "changes" because change implies a gradual transition from one form to another. The fossil record does not seem to confirm this."

Rapid appearance of new features is not a problem for biology. That the stickleback for example. Millions of years in the ocean, happy, then bam, stuck in freshwater because of the ice age. A rare allele that already exists in the wild is selected for. Rapid loss of armor. The accumulation of genetic diversity is slow, but often the event that causes selection is dramatic.

"Missing are all the failed evolutionary experiments one would think should be there."

How many dead failures do we expect to fossilize?Secondly, there are many many transitional fossils.

Even if you deny that, there are the nested hierarchies of molecular phylogeny to contend with. As well as conserved organelles, endosymbiosis, conserved biochemistry, etc....

"One thing I did read is that the body plan for an organism does not reside in the genome."

Where did you read this? Very questionable, and experimental investigation of Hox genes, for example, would disprove that. It is possible to alter genes in experimental organisms, with the result of altered body plans. Cloning might be another defense of this-the clone (generally) develops features solely from the donor of the nucleus. If not, where does that information reside? Why does the progeny of two Great Danes inherit a Great Dane body plan, and not develop as a Beagle?

"And if the genome specifies only proteins then mutations cannot account for new body plans."

? We are made up of proteins. They are the action end of biochemistry. Hair, muscle, the organic part of bones and teeth, all enzymes, all regulatory proteins. Proteins execute the functions encoded in nucleic acid.

All the changes you mentioned are relatively trivial, and may also be the result of a loss of function. E.G. antibiotic resistant bacteria do not do well when put in a petri dish with the original strain when there are no antibiotics present. And nylon eating in bacteria is the result of the original enzyme losing a lot of the original amino acids, and some efficiency. I don't know if you can extrapolate from this process the evolution of something really complex like an eye, or falgellum.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/